Evaluation of Genetic Diversity in Fish Using Molecular Markers

Dudu, Andreea; Georgescu, Sergiu Emil; Costache, Marieta

doi:10.5772/60423

Cited by 12 publications

(10 citation statements)

References 62 publications

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“…Molecular marker—in biology—is an expression for any stable heritable and detectable variation at the DNA level [ 5 ]. Molecular marker—on the gel image—is a polymorphic band that distinguishes between two groups of samples.…”

Section: Discussionmentioning

confidence: 99%

EgyGene GelAnalyzer4: a powerful image analysis software for one-dimensional gel electrophoresis

Ahmed

2021

Journal of Genetic Engineering and Biotechnology

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Background Gel image analysis is a cornerstone in electrophoresis-based experiments. Nature of the experiment determines the target of the analysis. Implemented features within different software for gel images and their outputs are variable. EgyGene GelAnalyzer4 software aimed to make a powerful, easy, and almost all-in-one software for gel image analysis. Results EgyGene GelAnalyzer4 is a software for analyzing the gel images. The program consists of six main parts: gel image enhancement, image analysis, data merging, molecular markers detection, phylogenetic tree prediction, and population parameters estimation. Firstly, the gel image enhancement part enhances the gel image colors and clarity. Then, the image is analyzed in the second part using both automatic and manual detection of lanes and bands. The third part, data merging, is for merging several analyses for different samples/gels together to produce one table comprises the entire experiment. The fourth section, markers detection, collects several pre-analyzed data for the same samples to detect their molecular markers based on some user-defined criteria. The fifth part uses the outputs of the previous parts to draw the phylogenetic tree between samples. The program constructs a phylogenetic tree using unweighted pair group method with arithmetic mean (UPGMA) method. Fourteen different equations are used to calculate the similarity percentages: Anderberg, Czekanowski, Dice, Faith, Gower and Legendre, Jaccard, Nei and Li, Rogers and Tanimoto, Russel and Rao, simple matching, Sokal and Michener, Sokal and Sneath 1, Sokal and Sneath 2, and Sorensen. The last section calculates the population parameters for the pre-analyzed images before. EgyGene GelAnalyzer4 is designed and programed using Microsoft Visual Studio 2012 Express version, based on the Dot Net FrameWork 4.5 edition, whereas its icons are created using the freeware Greenfish Icon Editor Pro 3.2.5.1. Conclusions EgyGene GelAnalyzer4 is a simple, fast, and user-friendly software with six novel features: changing the order of lanes within the gel image, splitting the detecting lane into two lanes, merging of several detected lanes into just one, splitting a single band into two bands, merging two or more bands to be a single band, and comparing data of several analyzed images with a big number of samples and merging it together in a single table and detection of molecular markers between samples. In addition to the basic features and outputs of other image analysis software such as calculation of relative mobility values, molecular weights/sizes estimation, DNA/RNA/protein quantity within bands, table of present/absent of bands, polymorphism percentage, similarity percentages and phylogeny, population parameters, enhancing the image colors and clarity, and merging data for several gels. In addition, writing names of samples and the detected markers on the image. EgyGene GelAnalyzer4 provides many several features, which may be not available together in any other alternative.

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Section: Discussionmentioning

confidence: 99%

EgyGene GelAnalyzer4: a powerful image analysis software for one-dimensional gel electrophoresis

Ahmed

2021

Journal of Genetic Engineering and Biotechnology

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“…At present, there are no specific SSR markers for the Alosa genus in the Caspian Sea. The usefulness of SSR markers depends on their polymorphism information content, which reflects the ability of a marker to detect a polymorphism in a given population (Dudu et al, 2015). We have demonstrated that the six SSRs found in American shad ( Alosa sapidissima ) (Julian and Bartron, 2007) show a high rate of polymorphism (PIC = 0.90) in A. braschnikowi as well.…”

Section: Discussionmentioning

confidence: 99%

Microsatellite Analysis of Five Populations of Alosa braschnikowi (Borodin, 1904) Across the Southern Coast of the Caspian Sea

et al. 2019

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Genetic diversity studies are essential in characterization of populations and species conservation. Alosa braschnikowi is a commercially valuable species native to the Caspian Sea. It is thought to have eight to nine subspecies, but the genetics of these populations remains to be investigated. The present study was performed to evaluate the genetic population structures of Caspian marine shad (Alosa braschnikowi) in the southern coast of the Caspian Sea using six pairs of SSR markers. A total of Alosa braschnikowi 140 specimens through five locations across the southern coast of the Caspian Sea were genotyped and 130 alleles were identified. The overall mean values of Ho and He were 0.58 and 0.87, respectively, with the highest and minimum value of Ho observed in Sari (0.67 ± 0.08) and Miankaleh (0.50 ± 0.04), respectively. The overall mean value of allelic richness was 12.6. The data suggest that there was a high rate of migration between populations of Alosa braschnikowi (overall mean of Nm = 13.57), with the highest value (19.07) between Gomishan and Mahmodabad locations. AMOVA results showed that 96% of variation was related to within populations and only 4% belonged to between populations. The mean Fst value of 0.019 indicates a low level of population differentiation. Our data suggest that there may be two genetically separate populations of Alosa braschnikowi across the southern coast of the Caspian Sea and a high rate of migration is likely to limit genetic diversity between them.

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“…Klasifikasi penanda kedua adalah yang berkaitan dengan posisi mereka di dalam sel. Jadi kita dapat membedakan antara penanda nuklir dan mitokondria DNA (mtDNA), tergantung pada lokalisasi mereka dalam genom nuklir atau mitokondria (Dudu et al, 2015).…”

Section: Keragaman Genetikunclassified

Keragaman genetik ikan lemuru (Sardinella lemuru) di wilayah perairan Indonesia

Hendiari

Sartimbul

Arthana

et al. 2020

AA: ASC

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Sardinella lemuru is pelagic commodities that has economic values for the Indonesian. S. lemuru has some major advantages, such as abundant population on Indonesian marine, low price, and has omega-3 for the human body. The high demands of lemuru fish cause a high rate of cached, that can cause the risk of population degradation. Proper management of these commodities are needed to decrease the risk impact, that can be done rightly based on the equal value of information, and one of them is genetic diversity. This research compiles the recent researches about the genetic diversity of Sardinella lemuru in Indonesia waters to get the explanation about lemuru fish diversity. The value of genetic diversity observed is based on the diversity value of Haplotype (Hd), because these two values have a positive correlation to make a whole representation from a commodity. The results of this review show that the genetic diversity of lemuru fish on Indonesian marine territorial has the high-value category. These results explain that in the high activities of fishing, lemuru fish genetically still have a high diversity that leads to the conclusion lemuru fish commodities has a high-level ability to adapt from environmental conditions.

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Evaluation of Genetic Diversity in Fish Using Molecular Markers

Cited by 12 publications

References 62 publications

EgyGene GelAnalyzer4: a powerful image analysis software for one-dimensional gel electrophoresis

EgyGene GelAnalyzer4: a powerful image analysis software for one-dimensional gel electrophoresis

Microsatellite Analysis of Five Populations of Alosa braschnikowi (Borodin, 1904) Across the Southern Coast of the Caspian Sea

Keragaman genetik ikan lemuru (Sardinella lemuru) di wilayah perairan Indonesia

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